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CHECK report for YAPSA on malbec1

This page was generated on 2021-05-06 12:29:42 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the YAPSA package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1968/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
YAPSA 1.16.0  (landing page)
Daniel Huebschmann
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/YAPSA
Branch: RELEASE_3_12
Last Commit: f344cdb
Last Changed Date: 2020-10-27 11:17:17 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: YAPSA
Version: 1.16.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:YAPSA.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings YAPSA_1.16.0.tar.gz
StartedAt: 2021-05-06 07:09:19 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 07:17:02 -0400 (Thu, 06 May 2021)
EllapsedTime: 462.7 seconds
RetCode: 0
Status:   OK  
CheckDir: YAPSA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:YAPSA.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings YAPSA_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/YAPSA.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘YAPSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘YAPSA’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘YAPSA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                          user system elapsed
confidence_indel_only_calulation        20.092  0.028  20.163
create_indel_mutation_catalogue_from_df 13.272  0.236  13.540
build_gene_list_for_pathway              4.736  0.088  20.963
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

YAPSA.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL YAPSA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘YAPSA’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (YAPSA)

Tests output

YAPSA.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.setenv(R_TESTS=" ")
> library(testthat)
> library(YAPSA)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: ggplot2
Loading required package: grid
> 
> test_check("YAPSA")
YAPSA:::shapiro_if_possible::error: Non-numeric inputYAPSA:::makeVRangesFromDataFrame::warning:strand  information missing, set to "+".
YAPSA:::makeVRangesFromDataFrame::in_PID.field found.  Retrieving PID information.
YAPSA:::makeVRangesFromDataFrame::in_subgroup.field found.  Retrieving subgroup information.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 62 ]
> 
> proc.time()
   user  system elapsed 
 14.712   0.432  17.298 

Example timings

YAPSA.Rcheck/YAPSA-Ex.timings

nameusersystemelapsed
GenomeOfNl_raw0.0080.0000.007
LCD0.0080.0000.007
LCD_complex_cutoff000
MutCat_indel_df0.0040.0000.003
SMC000
SMC_perPID000
add_annotation000
add_as_fist_to_list000
aggregate_exposures_by_category000
annotate_intermut_dist_PID0.0160.0000.016
annotate_intermut_dist_cohort0.0160.0040.021
annotation_exposures_barplot000
annotation_exposures_list_barplot000
annotation_heatmap_exposures000
attribute_nucleotide_exchanges0.0040.0000.002
attribute_sequence_contex_indel1.3640.0041.370
attribution_of_indels0.4040.0440.447
build_gene_list_for_pathway 4.736 0.08820.963
classify_indels0.0000.0000.001
compare_SMCs000
compare_exposures000
compare_expousre_sets0.0040.0000.003
compare_sets0.0040.0000.003
compare_to_catalogues000
complex_heatmap_exposures0.8280.0040.835
computeLogLik000
compute_comparison_stat_df000
confIntExp1.2160.0521.271
confidence_indel_calulation0.0000.0000.001
confidence_indel_only_calulation20.092 0.02820.163
correct_rounded000
cosineDist000
cosineMatchDist0.0040.0000.001
create_indel_mut_cat_from_df0.4240.0080.434
create_indel_mutation_catalogue_from_df13.272 0.23613.540
create_mutation_catalogue_from_VR1.2960.0361.335
create_mutation_catalogue_from_df0.9520.0521.009
cut_breaks_as_intervals0.1120.0040.115
deriveSigInd_df000
disambiguateVector000
enrichSigs000
exampleYAPSA0.0880.0000.091
exome_mutCatRaw_df0.0080.0000.010
exposures_barplot3.5560.0003.562
extract_names_from_gene_list000
find_affected_PIDs000
getSequenceContext0.1160.0000.114
get_extreme_PIDs0.0240.0000.023
hclust_exposures0.0080.0000.005
logLikelihood0.8000.0840.888
lymphomaNature2013_mutCat_df0.0000.0040.005
makeVRangesFromDataFrame0.1200.0000.117
make_catalogue_strata_df000
make_comparison_matrix0.0680.0120.081
make_strata_df000
make_subgroups_df0.0280.0040.030
melt_exposures000
merge_exposures000
normalizeMotifs_otherRownames000
normalize_df_per_dim0.0040.0000.008
plotExchangeSpectra000
plotExchangeSpectra_indel0.9320.0120.944
plotExposuresConfidence000
plotExposuresConfidence_indel000
plot_SMC000
plot_exposures0.3720.0000.372
plot_strata000
read_entry000
relateSigs000
repeat_df0.0000.0000.002
round_precision000
run_SMC4.0840.1084.195
run_annotate_vcf_pl000
run_comparison_catalogues000
run_comparison_general000
run_kmer_frequency_correction000
run_kmer_frequency_normalization000
run_plot_strata_general000
shapiro_if_possible0.0040.0000.001
split_exposures_by_subgroups000
stat_plot_subgroups000
stat_test_SMC0.0000.0000.001
stat_test_subgroups000
stderrmean0.0000.0000.001
sum_over_list_of_df0.0000.0040.002
temp_trellis_rainfall_plot1.5200.0001.685
testSigs000
test_exposureAffected000
test_gene_list_in_exposures000
transform_rownames_R_to_MATLAB000
translate_to_hg190.0040.0000.004
trellis_rainfall_plot1.5200.0081.531
trellis_rainfall_plot_old1.6360.0001.642
variateExp2.3640.0602.432
variateExpSingle0.8800.0160.898